Six Long Years
by leopardcrazy
Summary: What if scully left after "one son" and decided that the way mulder had treated her since diana arrived was unacceptable
1. Chapter 1

_I was very anti-Mulder after the episode "one son" and couldn't believe they created the episode "arcadia" just three episodes after. That somehow Mulder was just suddenly forgiven. I felt Scully deserved better and Mulder need a good wake up call. Well I am doing this story to give Scully more independence. Don't worry I still believe Mulder and Scully belong together but it shouldn't have happened after Diana died and suddenly Mulder is only stuck with Scully (like they made it seem in season 7). Well don't be too harsh on me, this is story is for me to deal with the arrogant side of Mulder. Oh and I am warning you now…grammar is NOT my friend. :)_

**Meeting in Kersh's Office:**

After Agent Spender defended his opinion that the only two people who should work on the x-files was Mulder and Scully, Kersh turned to them for an explanation on the happenings at El Rico Air Force Base.

"who burned those people" Kersh demanded

"they burned themselves with a choice made long ago by a conspiracy of men who thought they could sleep with the enemy. Only to awaken another enemy" Mulder answered while glancing at Scully for the last part, to admit his mistake.

Mulder thought that admitting his fault in choosing Diana over Scully would be enough to patch their damaged partnership. But little did he know that the partnership ended long ago when Scully said "…I cant help you anymore" at the guman's office. He did not know that Scully had already made plans to leave days before and that even Kersh and Skinner knew what Scully had planned; that the pitiful look Skinner gave him in that meeting was not over the burned bodies at the Base but because he knew the one person who stuck by him through everything was finally leaving. The straw that broke the camel's back had been placed.

After Kersh dismissed them, Mulder and Scully walked out of the room with bowed heads and an eerie feeling surrounded all the occupants. While walking down the hallway Scully told Mulder she was going home and would see him Monday morning. Mulder nodded and secretly hoped Kersh was now planning to assign them back on the x-files.

**Monday Morning: **

Mulder walked into the bullpen with two coffee cups in his hand and a cheery smile because he got a call this morning from Kersh saying that a meeting was being held to discuss the future of the x-files. Mulder was pretty confident that Kersh was going to hand them back the files. However, being lost in thought, Mulder failed to notice Scully's desk was empty and now the smile was wiped off his face. Mulder came to the conclusion the Scully had already headed for Kersh's office and ignored the pressure in his chest. When Mulder entered Kersh's office he was surprised to see Diana sitting in one of the seats.

"Sit down Agent Mulder" said Kersh. Mulder immediately took the seat next to Diana.

"It has come to my attention that Agent Spender and Agent Scully firmly believe that you belong on the X-files and I will not go against their wishes. You and Agent Fowley will continue to investigate x-file cases, you can now move your belongings back to the basement office and settle in. Tomorrow I will present you two with a new case. That will be all Agents. You are dismissed."

Mulder was in shock. He couldn't move. At first he was elated that he was getting the files back, his life's work was now in his hands. But soon he realized that Scully was no longer his partner and that Scully had already been informed.

"I am sorry sir but I cannot accept your decision. Agent Scully deserves to be put on the x-files just as much as I do"

"Agent Mulder this is not a choice I am asking you to make. You will be assigned to the X-files and will be partnered with Agent Fowley. Unless you want to be dismissed from the FBI completely, I would recommend that you accept this. And not that it is any of your business but Agent Scully has already made future occupational plans and has no longer desired to be partnered with you. Now agents you are dismissed!"

Mulder could not believe what Kersh was saying…Scully no longer wanted to be on x-files?? Was he crazy? This was her life's work just as much as his. But he knew he could no longer argue with Kersh and briskly walked out behind Diana.

"Diana I am going to go see where Scully is to discuss this. I'll see you tomorrow morning"

"She is not in the building Fox, I saw her leave a few hours ago"

"Well she must be at home, im going to stop by and then ill come back to gather my things and bring It down to the basement. Thanks for telling me, it saved me some time to look for her"

Mulder pulled up to Scully's building and headed straight for her apartment building. He knocked for a few minutes and when he didn't hear any movement he fished his pocked for his key. He opened the door and was presented with an empty apartment building. Nothing was there. The walls were bare, there were no boxes, no lint on the carpet, no furniture, and most importantly no Scully. Mulder looked at the back of the door to make sure he was at the right apartment number but knew he was if the key fit.

"hey Mr. Mulder, why are you looking for Dana here?" the building manger asked. Curious to see why Dana's door was left open.

"huh? Oh why is her apartment empty"

"what? You mean you don't know she moved?"

"no! when did she plan this! Am I in some parallel universe…what the hell is going on!"

"im sorry Mr. Mulder I assumed you knew. Umm…Dana told me she was leaving a couple of days ago. so many people were helping her move that I figured she was finally moving in with you"

"what! Who was helping her move! And when did she tell you this exactly…I need the date"

"Her mother, those geeky men, and that big buff guy who I think is your boss came to help her and I don't know the date but I remember it right after I had to let her in her building because she didn't have her key. Something about a quarantine procedure"

Mulder couldn't believe that the guman, skinner and maggie knew Scully was leaving and never gave him any indication. Mulder went to each of their houses and was rewarded with the same response "im sorry we can't help you, but it was her decision and we have to respect that." No one gave him any information about her whereabouts and was basically given the cold shoulder. Mulder had no idea that the next time he would see Scully again would be two years later.


	2. Chapter 2

_Well I'm glad I'm not the only one with strong feelings about this episode. Thank you for the positive reviews. I can only make readers happy if they review or email me to give me their insights or wishes on how the next chapter should be…so just let me know. Well this is how I pictured it….hope you like it. Oh don't freak out too much on this chapter…things will work out ;) _

**Two Years Later: **

The X-file division is still being investigated by Agents Mulder and Fowley but has not received the creditability and respect it had in those six years when Scully was assigned. No one at the FBI building really hears or sees these two agents but two things are for certain: Mulder and Diana are in a relationship and they continue to investigate files in the basement, other than that no one knows anything or really cares.

Mulder was curious as to why he got a phone call this morning from Skinner saying a meeting was being held to discuss the x-files. He figured it was probably just time to shut them down; they had only investigated crappy files anyways and were just screwing around. Mulder couldn't figure out how his life had turned upside down so fast, but since he has been following the same routine for two years he figured it was now too late to stop and think about it. At this time, Diana entered the basement office with breakfast.

"Hey fox, I figured since the meeting doesn't start till ten minutes we could scarf this down and then go upstairs with at least a full stomach to help us survive Skinner's glare"

"That's sounds good Diana. I don't know what I would do without you" Mulder automatically replied

Ten minutes later Mulder and Diana entered Skinner's office but did not see the usual two seats in front of his desk ready for a reprimand. Instead, it was turned into a conference room and there were at least twenty agents in attendance.

"Agents Mulder and Fowley have a seat, the meeting will begin shortly. We are just waiting on Agent Mathews who will address the panel" boomed Skinner

Mulder and Diana immediately went to the two empty seats at the far corner of the room. Diana chatted on and on about their plans for the weekend and if they should move in together so they could start to build a family.

"Oh fox I'm so excited! If the x-files are closed then we can actually have time to raise this baby. I know we were a little worried that I was two weeks late and how our lifestyle leaves no room for an infant but now…wow we can get married and have that dream house we use to talk about when we were first partnered together. I should get a phone call from my doctor later today to confirm that I really am pregnant."

Mulder tried to keep the smile on his face but he couldn't help but groan at the idea of having a baby, it was too much of a reminder of Scully and that IVF procedure she had done. God how different things could be if that was actually was successful? They would have a baby together that would be over three years old…

His thoughts were interrupted by the sounds of doors opening and a few whispering words. When he looked up he saw a pair of FBI agents walking through. The male agent was tall compared to his petite partner. She had medium length blonde hair and was whispering in Skinner's ear. Her partner must have been close to her because he had his hand on her arm and seemed to need contact. Mulder couldn't help grin at the how similar they were to him and Scully. It was almost like looking in a mirror.

"Take your seats agents and give your full attention to Special Agent Dana Mathews" ordered Skinner

Mulder heart couldn't stop pounding after name "Dana" passed through Skinner's lips. The first logical explanation was that there was another agent with Scully's first name…it was fairly common. But once he saw her step and face the panel of agents, Mulder knew he was now face to face with Dana Scully. Her hair color might have changed but she still had those piercing baby blue eyes that could make drown him for hours. Once Mulder got over the fact that his past had once again walked back into his life, the other dramatic changes that Dana Scully underwent were now being processed. She looked a little thinner almost parallel to her cancer days, her face was free of the bags and blackness she use to have under her eyes and she was dressed much differently. Her suits were no longer the conservative type which made suspects and fellow colleagues pay attention to her intelligence rather than her womanly figure. Instead, she was wearing a tight dark blue skirt suit which by the way he could figure…the skirt had barely made the Bureau length requirement. She didn't have those clunky black heels but instead thin stilettos and the blouse under her fitted to perfection jacket was bright and in his opinion had too many buttons undone. Even with all these changes Mulder could get past the hair or the fact that she had a partner who wasn't him...

The voice that Mulder had not heard from in over two years was now sweeping through his senses. "Thank you for attending this rather vague meeting. Before I go into details on why you are all here today, I want to introduce myself. Only a few of you in this room recognize me and have worked with me, but all of you should be familiar with the reputation I had on the X-Files. Skinner introduced me as Dana Mathews but my maiden name is Scully and I worked with Agent Mulder for about six years. I know my whereabouts were a little vague and I want to shed light on that aspect."

Of course there were a few gasps in the room when the identity of the speaker was finally addressed and many of the agents started to rudely murmur their own questions and theories as to why Scully had finally left. Scully could no longer take the constant whispering and decided to take the best approach: confrontation.


	3. Chapter 3

_Well since "mooonbeams" updated her story… I guess I need to follow-through on our agreement. This chapter might be a little weird…it's basically all Scully dialogue. I felt she needed to let a lot of feelings out that she had bottled up during the years. I know it's not really appropriate to tell a room full of twenty agents your personal business but this gives me more drama…I love it when Mulder/Scully are the topic of conversation and gossip! :)_

"Alright let's just get everything out in the open, shall we! Now what rumors have been circulating around the water cooler during those two years I've been gone? If I had to guess, I would suspect that since you all thought I had been sleeping with Agent Mulder for years, that either he had cheated on me with Agent Fowley or I was a jealous prude who wish she got some??"

The deafening sound of silence circulated the room and intimidated every single individual. The sounds of crickets chirping would have been a blessing. Even Skinner was in shock. This was clearly a "new" Scully and no one was brave enough to question it.

"Well come on! Let me hear the gossip! Does anyone have the balls to ask me what you all are thinking or what your suspicions are? I want to be open with every individual in this room…I will need to gain your trust in the future, so we might as well start with my personal life."

Special Agent Chris Halpert was the only one in the room to step up to the plate. "Yeah I…well "we" are all dying to know why you suddenly left. Recently, I have been assigned to read a few of the files you and Agent Mulder investigated throughout the years and from a brief glace, I came to the conclusion that you went through some pretty tough shit but had never even considered leaving. If that wasn't bad ...I am hard pressed to see what could be worse"

"Thank you Chris, I now have a new found respect for you. I figured that is what everyone probably thought. I left for many reasons and some of which are those you just mentioned. But let me just get one thing straight…I did not leave because Agent Fowley entered the picture. Oh sure, she was a part of it…and did give me more of an incentive to leave. But there is only one reason for me to leave and I would think that would be fairly obvious. After everything I have been through, those incidents of horror I had witnessed on the X-files never made me blink; I took the hits with pride and always continued on. There is only one person who can make me leave and as you all expected, that person is Agent Mulder. He did make me leave…but not with his words but with his actions."

Deep Sigh...

"I had been on the X-Files for six years and after a string of incidences I came to the conclusion that my dedication to those files would never measure up…they would never be enough. In those six years I have been abducted, three months of my life were taken from me. I had procedures performed on me that I will never fully understand what exactly was done. My sister was killed in my place. I was given cancer because I took out a chip that monitored me, then I had to put another chip back in to cure my disease. I had to live a life under "their" control. I found out that "they" were creating children using my ova and alien DNA to experiment on and were basically a ticking clock; I had to watch one of my biological children die right in front of my eyes. Then I had to find out I could never have children of my own because of what was done to me. I have lied in court and put in jail because I wouldn't reveal the location of my partner. I was given an alien virus and sent to Antarctica to die because of that infection. I lied multiple times, almost died more times than that, and sacrificed my family and social life. But I never regretted my decision to stay. I felt it was worth the price."

"All I wanted in return was trust. I felt I deserved to have my partner's trust after everything I had went through. I had proven myself over and over, showing I was loyal; that I had lost just as much as he…maybe more. And what happened after I decided not to back Agent Mulder one time during an OPR meeting of the Dallas Bombing, because that proof I found supported a new theory that was different from Agent Mulder's? To Agent Mulder, that was the ultimate betrayal. He made a decision that day; he took the side of a woman who has never sacrificed anything but maybe her integrity, over my own. Just because she would admit she saw an "alien" and I would never admit that. Being a believer was worth the trust of a man who told me to "trust no one". That day I realized Agent Mulder didn't want me, he wanted someone who claps in the stands…not someone who actually goes out on the field to play. The day when Agent Mulder asked if I wanted him to "make a choice" I made a choice of my own. I decided I could no longer be his partner. I started to make steps to transfer. After the incident at El Rico, I had Mulder make another choice. If he didn't support me I would leave at that moment. I was always waiting for the right time to leave and the incidents that went on that day…well let's just say it was the sign I was waiting for."

"My whole partnership with Mulder is based on one thing: Trust. It all started out on the Gibson Praise case, when an individual entered the picture and Mulder couldn't even give me the respect as fellow colleague to tell me that he previously worked with her on the exact same files I had put six years of my life into! I had to learn from an outside source. And for basically a year, Mulder never mentioned Agent Fowley or the significance she had on the files or in his life. It was just one big elephant in the room. Then the ditches started to happen again and we were put on desk duty as punishment, which I had to do most of the work."

"I am not some man's secretary or floor mat to walk on. I felt I deserved better…hell I did deserve better and I was not about to wait till the light bulb in Mulder's head turned on. It should have happened immediately. The fact that Mulder could not see how he was treating me: shoving me out and bringing in the next new thing…well that did it. I had to move on and find my own salvation because it certainly wasn't going to come from him. He could treat the women who left him and returned years later much better than me. (Harsh chuckle from Scully) If that's the case…Agent Mulder will probably treat me like a queen today, since I stood by his side for far longer and only left for a few years"

Every single person in that room was in awe. This woman, who had sacrificed everything, only wanted one thing in return and could not even receive it. They couldn't believe she didn't leave sooner. But now it was obvious why she didn't, she was in love. The only three agents who were women (besides Agent Fowley) shot daggers and ice stares at Mulder during every crucial and heartbreaking moment in Agent Scully's speech. Not only did Mulder have to suffer through that whole ordeal but had to survive the guilt stares he was given by the men too. Mulder knew he was in deep shit and was almost certain that it was too late to fix it.

_The next chapter will reveal what Scully has been doing for two years. I did give a small little hint in Scully's speech. But I bet you guys didn't catch it. Well I'll probably post a new chapter every weekend. I have no motivation during the week with school, I prefer to read stories that others have posted. :) Thanks for the reviews and I hope the writers out there will continue. _


End file.
